Cho Jung-tai's comments came after a Chinese man was found in a rubber dinghy in waters near northern New Taipei City on Saturday, following a similar incident in June.
"We have already been reviewing some cases in the past and perhaps this incident has made us feel that we must speed up," Cho told reporters.
"I can promise that ensuring national security is the unshakeable responsibility of the government. We must quickly review these incidents and make appropriate preparations".
The coast guard said it was notified by the New Taipei fire department early Saturday that a man was spotted near the Houkeng River estuary about 100 metres (328 feet) from the shore.
Coast guard personnel pulled the Chinese national ashore and sent him to hospital for treatment for severe dehydration.
The man, who claimed he "has debts in China and wants to start a new life in Taiwan", according to the coast guard, was later detained for attempting to enter the island without permission.
China claims democratic Taiwan as part of its territory and has in recent years ramped up military and political pressures on the island.
Last month, Taiwanese prosecutors indicted a former Chinese naval captain arrested for illegally entering Taiwan by boat, but they said "no military or national security involvement" was linked to his act.
He was picked up by the coast guard in June after his vessel collided with other boats on the Tamsui River, which flows from the capital Taipei to the island's northern coast.
Officials said he was one of 18 purported defectors from China seen over the past year or so.
They all claimed to admire Taiwan's "democratic way of life", authorities said, who also warned they could not rule out the possibility the incursions were a test of the island's defences by China.
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